Yeast genome analysis on a SGI Supercomputer - demonstration project.

Reinhard Schneider schneider at embl-heidelberg.de
Thu Feb 29 15:58:37 EST 1996


GeneCrunch: See genome analysis on a supercomputer as it happens.
Watch the analysis of genome information live on the WWW, March 4-7,
1996.

In a joint demonstration project between Silicon Graphics and scientists 
from the EMBL-Heidelberg/EMBL-EBI the GeneQuiz software system will
analyze 
more than 6000 protein sequences from the genome of yeast (Saccharomyces 
cerevisiae) on a 64 processor SGI POWER CHALLENGEarray in just a few
days.

The project will demonstrate large-scale genome sequence analysis on an 
almost-complete set of yeast genes. The analysis will be repeated as
soon 
as the international collaborative effort of yeast researchers releases
to 
the public the complete genetic blueprint of yeast, scheduled for later 
this year.

The results on the likely biological function of many new genes will 
be of interest to biological researchers in both academia and industry. 
The results will be published on two internet Web sites as the analysis 
progresses, starting March 4th, 1996:

        http://genecrunch.sgi.com    http://genecrunch.sgi.ch

In addition to the biological results of the analysis, the sites will 
also contain information describing the  supercomputing and web
technology 
used.

GeneQuiz is an automated system for large-scale genome sequence
analysis.
It aims at adding value to biosequence information by predicting the 
biological function of the corresponding genes. GeneQuiz accesses
up-to-date
protein and DNA databases, derives information  by sophisticated search
and
analysis methods, and interprets any findings in terms of biological
function 
using expert rules.
It also predicts three-dimensional structures of protein molecules when 
these can be inferred by homology . The predicted functions are made
available 
in hyperlinked WWW tables and the predicted coordinates of 3D structures
in 
Protein Data Bank format. GeneQuiz is a collaborative effort between the
two 
EMBL institutes and former EMBL  scientists at CNB Madrid, MDC Berlin,
and 
SRI Meno Park.

The POWER CHALLENGEarray used for this project is located at the Silicon
Graphics European Supercomputing Technology Center in Cortaillod,
Switzerland. The POWER CHALLENGEarray consists of 4 POWER CHALLENGE
nodes 
each with 16 R8000 Processors linked together with the very fast HIPPI 
interfaces.


Reinhard Schneider and Georg Casari
Biological Structures and Biocomputing program
EMBL-Heidelberg

Chris Sander
European Bioinformatics Institute
EMBL-EBI



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